staden 2.0.0b1 on ubuntu 9.04

2009-09-18
2013-04-18
  • Hi to all,

    I installed staden 2.0.0b1 on ubuntu 9.04 without problems, I followed the instructions to convert a gap4 db to gap5. gap5 now can open my database apparently without problems, some features work and it seems really nice; the problems start when I use the scroll bars to navigate windows such as contig editor or template display, the program crashes without any advice.

    Can you give me some help?

    thank you in advance,

    Giuseppe D'AUria

     
  • James Bonfield
    James Bonfield
    2009-09-18

    I have a 32-bit vmplayer instance of ubuntu-9.04 to test on, but haven't noticed such issues. The scrollbars work just fine in both editor and template display. (Well, the virtual scrollbar in the template display is sometimes a bit "willfull", but it doesn't crash.)

    I did however spot a bug where moving the mouse over the reading names in the editor sometimes caused a crash. I'm investigating that currently.

     
  • Thank you, I forgot that I am on a 64bits machine.

    After calling gap5 I can see:

    check_database -io io=0x9448a0
    register with .e1.ed1.pane.seq.sheet
    Event 'REGISTER {id 1} {type TYPE_UNKNOWN} {contig 5}' not handled
    Deregister 1
    Resizing HacheTable tg_cache to 4096
    register with .e2.ed1.pane.seq.sheet
    Event 'REGISTER {id 3} {type TYPE_UNKNOWN} {contig 11}' not handled
    *** buffer overflow detected ***: stash terminated
    ======= Backtrace: =========
    /lib/libc.so.6(__fortify_fail+0x37)
    /lib/libc.so.6
    /lib/libc.so.6
    /lib/libc.so.6(_IO_default_xsputn+0x96)
    /lib/libc.so.6(_IO_vfprintf+0x1c1c)
    /lib/libc.so.6(__vsprintf_chk+0x99)
    /lib/libc.so.6(__sprintf_chk+0x80)
    /home/gdauria/Downloads/staden-2.0.0b1-src/lib/libgap5.so
    /usr/lib/libtcl8.4.so.0(TclInvokeStringCommand+0x6b)
    /usr/lib/libtcl8.4.so.0(TclEvalObjvInternal+0x323)
    /usr/lib/libtcl8.4.so.0
    /usr/lib/libtcl8.4.so.0(TclCompEvalObj+0xff)
    /usr/lib/libtcl8.4.so.0(TclObjInterpProc+0x21d)
    /usr/lib/libtcl8.4.so.0(TclEvalObjvInternal+0x323)
    /usr/lib/libtcl8.4.so.0(Tcl_EvalEx+0x427)
    /usr/lib/libtk8.4.so.0(Tk_BindEvent+0x78f)
    /usr/lib/libtk8.4.so.0(TkBindEventProc+0x195)
    /usr/lib/libtk8.4.so.0(Tk_HandleEvent+0x4f1)
    /usr/lib/libtk8.4.so.0
    /usr/lib/libtcl8.4.so.0(Tcl_ServiceEvent+0x82)
    /usr/lib/libtcl8.4.so.0(Tcl_DoOneEvent+0x97)
    /usr/lib/libtk8.4.so.0(Tk_MainLoop+0x22)
    /usr/lib/libtcl8.4.so.0(Tcl_Main+0x1f6)
    stash
    /lib/libc.so.6(__libc_start_main+0xe6)
    stash
    I do not really thing is due to the scrolling, some time it crash with a similar output without any particular reason.

    I found gap5 really fast and I will be happy to use it with my new big 454 assembly projects

    Thank you in advance,

    Giuseppe

    PD probably is not the correct way to past an output..

     
  • James Bonfield
    James Bonfield
    2009-09-18

    So that error is coming from the automated buffer-overrun code which is enabled in Ubuntu. I've found one recently in gap5/tkEdNames.c (see the svn repository for the latest) which was affecting name highlighting in the editor.

    So this happens when you try to scroll in X in either the contig editor or template displays? Does it happen only on one specific data set or on seemingly all of them?

    If you start gap5 in the background (add & after the command line) you may be able to gather more debugging. Use (assuming installed) gdb -pid *num* where *num* is the gap5 process ID (listed as "stash" under ps") and then "c" to continue. Once it crashes gdb will then interrupt it and hopefully allow you to type "where" to get a full stack trace.  This would help in tracking down the bug, but if you're not comfortable with debugging this way then no problem - I'll have a poke around myself too and try to reproduce it.

    Note that you can turn off this overflow detecting in the compiler.  Warning - this is NOT a fix, it's more of a way to sweep it under the carpet. Obviously I need to track down this particular bug you've found.

    Anyway, to disable it edit system.mk and modify the "*CC=gcc*" line to be "*CC=gcc -D_FORTIFY_SOURCE=0 -fno-stack-protector*".

    Thanks,

    James

     
  • James Bonfield
    James Bonfield
    2009-09-18

    Oh I forgot to add - changing the system.mk file will have no effect until you recompile it, so you'll need to do "make clean", "make" and "make install" again.

     
  • I just reinstalled it and seems to works, I have the same problem of the crash on mouseover on reading names…. do you solved this problem?

    Another question… I can not found the really helpful ReadPairs utilities….. where are they????…. I desperately need these to work with my PE assemblies.

    Thank you in advance

    GIuseppe